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Confounded by the inexhaustible array of choices available when you stroll through a supermarket today? Well, here's another one to add to the list: How would you like your environmental degradation? By land or by sea? Whether it's pesticides and fertilizers leaching out of croplands or marine fish stocks vanishing by the boatful, every food purchase carries increasingly visible ecological costs.

Against this backdrop, a growing cadre of academics, farmers and aquaculturists is working to refine and popularize a technique that could slash those costs for both fish and vegetable products. The technique, dubbed "aquaponics," integrates fish farming and hydroponic agriculture in a sort of closed, symbiotic loop—the fish serve as fertilizer factories, the plants as water purifiers. The idea is to maximize food production while minimizing environmentally taxing inputs and potentially polluting outputs—a sustainable approach to growing healthy food.

At Cabbage Hill Farm in Mount Kisco, N.Y., a sizable aquaponic greenhouse offers an established proof of concept.

Six cylindrical tanks ranging in size from 1,000 to 3,200 gallons (3,785 to 12,100 liters) line the north side of the building, each home to hundreds of edible fish such as bass or tilapia. As the fish respire, their gills excrete ammonia into the water. Ammonia is a normal metabolic by-product but is toxic in sufficient concentrations, so it must be removed to keep fish healthy.

The key to aquaponics is that this waste is put to good use: In a churning bioreactor resembling a giant blue cauldron, ammonia-laden water drawn from the nearby tanks is processed by colonies of two helpful bacteria, Nitrosomonas and Nitrobacter. The former turns ammonia into nitrite, which the latter then converts to nitrate, a potent fertilizer. By using fish excretions to feed plants, "you don't have to buy all these fertilizers that are made from petroleum products and that take energy" to produce and transport, says agricultural scientist James Rakocy of the University of the Virgin Islands (UVI), a longtime proponent of aquaponics who has a demonstration facility at his institution. "Our fertilizer would be a waste product; instead we're using it to grow plants."

Growing food crops at Cabbage Hill takes place in long, shallow tubs on the south side of the greenhouse, which are filled with newly nutritious water from the bioreactor. On so-called rafts (repurposed polystyrene insulation panels) floating in the tubs, basil, bok choy and lettuce plants grow hydroponically—that is, without soil—their bare roots dangling through holes in the rafts to draw nutrients directly from the water below.

Stripped of its nitrate, the water is ready for return to the fish tanks, having essentially been filtered by the roots of fast-growing, edible, high-value plants.

Cabbage Hill's resident aquaponic guru, Kevin Ferry, views the process as an extension of natural nutrient cycles. "All we're doing is speeding up nature—the bioreactor is just composting," he says, comparing the churning aeration inside the cauldron with the turning of a compost pile.

As with any attempt to accelerate or enhance nature, aquaponics has costs and complications. During a tour of Cabbage Hill's facility, Ferry stops frequently to tinker with the systems—tossing handfuls of feed into a tilapia tank, adding lime to the bioreactor to bring up the water's pH (reduce its acidity), dipping his fingers into a bass tank and tasting the water to gauge its salt content (about eight parts per thousand, his taste buds register). "A place like this can't be left alone for very long," he acknowledges.

Behind the building, a biodiesel generator and waste vegetable oil boiler, both dormant during the summer months, attest to the aquaponic system's thirst for energy—the pumps, filters and bioreactor run year-round at a sometimes deafening whir, and the winter brings a need to heat the tanks and power overhead lights, as well.

These demands make it tough to compete with foreign and industrial-scale aquaculturists on the metrics of price and size alone. (Luckily, the fast-growing vegetable crops are the primary moneymaker.) Cabbage Hill's customers are mainly local restaurants and markets that prize what Ferry refers to as "farm-to-table" relationships. "These systems are fairly expensive," Rakocy notes. "So you have to raise really high-value crops and look for niche markets."

Rakocy has sought to drive down the price of aquaponics by developing projects that run on waste energy. UVI was part of a consortium that, with the help of a $150,000 grant from the U.S. Environmental Protection Agency in 2001, built a landfill gas–powered aquaponic facility at Rutgers University's EcoComplex, a research center at the Burlington County, N.J., landfill. "In the future," he says, "I could see aquaponics setups ringing landfills," mining their waste gas to produce food.

Even in its present energy-hungry state, Rakocy points out, aquaponics has an advantage in the preservation of another precious resource: water. Much of the irrigation water in traditional agriculture runs off the soil or evaporates before it reaches the roots. In a recirculating aquaponic setup, by contrast, "the plants just take what they need, and the rest stays in the system and goes back to the fish," he says. In fact, the UVI system is so efficient that its occasional losses are entirely replenished by a rainwater catchment system, Rakocy adds.

Martin Schreibman, a biologist at Brooklyn College in New York City and an advocate for urban aquaculture, concedes that aquaponics poses myriad challenges but, like Rakocy, he sees the tank as half full. "Every revolution had its own problems: the Industrial Revolution, the Green Revolution, the agricultural revolution," he says. "Now the blue revolution that people are talking about, sure it has problems, but you can get around them. I think these are problems that are resolvable."

In fact, Schreibman adds, adopting aquaponics near population centers could present solutions to other intractable problems. "Natural fish stocks are all depleted, we have problems with tainted food coming in from abroad, we have unemployment here, we have a bad economy," he says. "This kind of urban aquaculture and urban aquaponics addresses these questions."

Schreibman notes that criticism of the energy requirements for aquaponics plays down "the energy that's used boating something from China or flying it up from Ecuador," two of the primary importers of seafood into the U.S. "So it's a trade-off. We're not trucking it miles."

As fuel prices for imports rise and more and more environmental issues linked to food production come to light, the level of interest in aquaponics is "increasing astronomically," Rakocy says. He leads a short course at UVI on aquaponic methods, for which he says attendance has more than doubled from 33 to 73 students in the past three years. "This year we had to reject a bunch of people," Rakocy says. "I've been getting so many inquiries saying, 'Put me down on the waiting list for next year.'"